Table of contents


In This Issue

In this issue ppvii - viii




Tilting toward secrecy p1055


A European high court ruling on the patentability of inventions related to human embryonic stem cells could promote secrecy and reduce access to data and cell lines.

European court bans embryonic stem cell patents pp1057 - 1059

Nuala Moran


Conflicts of interest go online p1058

Gunjan Sinha


Shutdown by auction p1060

Brian Orelli


GlaxoSmithKline malaria vaccine phase 3 trial heralded pp1060 - 1062

Simon Franz


Interest groups jostle to influence PDUFA V p1062

Jeffrey L Fox


Industry continues dabbling with open innovation models pp1063 - 1065

Cormac Sheridan


Cold-tolerant trees win p1063

Emily Walt


Around the world in a month p1065


Jackson's $1.1 billion makeover p1066

Jennifer Rohn


Near-record drug approvals p1066

Jeffrey L. Fox


New startup models emerge as investor landscape shifts pp1066 - 1067

Brady Huggett



Zafgen p1068

Jennifer Rohn


Zafgen hopes that small-molecule targeting of methionine aminopeptidase 2 (MetAP2), an enzyme originally associated with tumor angiogenesis, will lead to a new anti-obesity drug.



Shape shifting pp1069 - 1071

Bob Baltera


Faced with limited funding and the need to find the most time- and cost-efficient route to proof of concept and relevance, how should you reorganize your company to facilitate development of your most valuable assets?


Opinion and Comment


Generation of the potent anti-malarial drug artemisinin in tobacco pp1072 - 1074

Moran Farhi, Elena Marhevka, Julius Ben-Ari, Anna Algamas-Dimantov, Zhuobin Liang, Vardit Zeevi, Orit Edelbaum, Ben Spitzer-Rimon, Hagai Abeliovich, Betty Schwartz, Tzvi Tzfira & Alexander Vainstein


Relative potential of biosynthetic pathways for biofuels and bio-based products pp1074 - 1078

Deepak Dugar & Gregory Stephanopoulos


Re-evaluating PARP1 inhibitor in cancer pp1078 - 1079

Alexei Tulin


Access to human embryonic stem cell lines pp1079 - 1081

Aaron D Levine


Sarbanes-Oxley overburdens biotech companies pp1081 - 1082

Mark Kessel




What's fueling the biotech engine—2010 to 2011 pp1083 - 1089

Saurabh Aggarwal


In the past year, biologics sector sales grew by single digits, driven by monoclonal antibodies and insulin products. New product launches are showing mixed results and are facing rising challenges from changes to reimbursement policies.


Agricultural microbial resources: private property or global commons? pp1091 - 1093

David Kothamasi, Matthew Spurlock & E Toby Kiers


Agricultural microbes have become an attractive target for patenting, but the lack of a consistent global patent regime and increasingly heated debates over microbial ownership rights are barriers to the development of this resource.


News and Views

Dissecting cancer heterogeneity pp1095 - 1096

David Dornan & Jeff Settleman


Transcriptional profiling of single cells in colon tumors may enable prediction of patient outcomes.

See also: Research by Dalerba et al.

Genomic rearrangement in three dimensions pp1096 - 1098

PJ Hastings & Susan M Rosenberg


Two studies illuminate why genome rearrangements in cancer cells occur where they do.

See also: Computational Biology by De & Michor | Computational Biology by Fudenberg et al.

The new landscape of protein ubiquitination pp1098 - 1100

Guoqiang Xu & Samie R Jaffrey


Proteome-wide identification of ubiquitination events reveals their functional classes and identifies substrates for ubiquitin ligases.


Research Highlights


Computational Biology


DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes pp1103 - 1108

Subhajyoti De & Franziska Michor


Copy-number changes in cancer genomes may be caused by errors during the replication of colocalized DNA regions. De and Michor provide genome-wide evidence for this model by integrating data on DNA replication timing, the three-dimensional organization of the genome and copy-number alterations in cancer.

See also: News and Views by Hastings & Rosenberg

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer pp1109 - 1113

Geoff Fudenberg, Gad Getz, Matthew Meyerson & Leonid A Mirny


Copy-number changes, point mutations and rearrangements are all usually found in cancer genomes, but their relative frequencies are highly variable. Using statistical approaches to model different processes, Fudenberg et al. find that copy number gain and loss is influenced by the three-dimensional organization of the genome in the nucleus.

See also: News and Views by Hastings & Rosenberg



Brief Communications

In silico feedback for in vivo regulation of a gene expression circuit pp1114 - 1116

Andreas Milias-Argeitis, Sean Summers, Jacob Stewart-Ornstein, Ignacio Zuleta, David Pincus, Hana El-Samad, Mustafa Khammash & John Lygeros


Creating synthetic biological circuits can be maddeningly difficult because of unpredictable stimuli and unknown variability in the system. Milias-Argeitis et al. circumvent these problems by moving control functions outside the cell—to a computer—and connecting computer and cell through optogenetics.

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells pp1117 - 1119

Kitai Kim, Rui Zhao, Akiko Doi, Kitwa Ng, Juli Unternaehrer, Patrick Cahan, Huo Hongguang, Yuin-Han Loh, Martin J Aryee, M William Lensch, Hu Li, James J Collins, Andrew P Feinberg & George Q Daley


Mouse induced pluripotent stem (iPS) cells have been shown to retain an epigenetic 'memory' of their cell type of origin. Kim et al. study this question in human cells and document both incomplete erasure of methylation and aberrant de novo methylation during reprogramming.


Single-cell dissection of transcriptional heterogeneity in human colon tumors pp1120 - 1127

Piero Dalerba, Tomer Kalisky, Debashis Sahoo, Pradeep S Rajendran, Michael E Rothenberg, Anne A Leyrat, Sopheak Sim, Jennifer Okamoto, Darius M Johnston, Dalong Qian, Maider Zabala, Janet Bueno, Norma F Neff, Jianbin Wang, Andrew A Shelton, Brendan Visser, Shigeo Hisamori, Yohei Shimono, Marc van de Wetering, Hans Clevers, Michael F Clarke & Stephen R Quake


Not all cells in a tumor are alike, but our ability to characterize cancer heterogeneity in detail has been limited. Dalerba et al. use high-throughput single-cell expression analysis to define clinically relevant subpopulations in normal and cancerous colon tissue.

See also: News and Views by Dornan & Settleman


Efficacy of genetically modified Bt toxins against insects with different genetic mechanisms of resistance pp1128 - 1131

Bruce E Tabashnik, Fangneng Huang, Mukti N Ghimire, B Rogers Leonard, Blair D Siegfried, Murugesan Rangasamy, Yajun Yang, Yidong Wu, Linda J Gahan, David G Heckel, Alejandra Bravo & Mario Soberón


The benefits of crops that produce insecticidal toxins from Bacillus thuringiensis (Bt) are threatened by the emergence of insect resistance. Working with five major crop pests, Tabashnik et al. show that previously described variant Bt toxins kill pests rendered resistant to native Bt toxins by multiple mechanisms.


Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage pp1132 - 1144

Katherine Amps, Peter W Andrews, George Anyfantis, Lyle Armstrong, Stuart Avery, Hossein Baharvand, Julie Baker, Duncan Baker, Maria B Munoz, Stephen Beil, Nissim Benvenisty, Dalit Ben-Yosef, Juan-Carlos Biancotti, Alexis Bosman, Romulo Martin Brena, Daniel Brison, Gunilla Caisander, María V Camarasa, Jieming Chen, Eric Chiao, Young Min Choi, Andre B H Choo, Daniel Collins, Alan Colman, Jeremy M Crook, George Q Daley, Anne Dalton, Paul A De Sousa, Chris Denning, Janet Downie, Petr Dvorak, Karen D Montgomery, Anis Feki, Angela Ford, Victoria Fox, Ana M Fraga, Tzvia Frumkin, Lin Ge, Paul J Gokhale, Tamar Golan-Lev, Hamid Gourabi, Michal Gropp, Lu Guangxiu, Ales Hampl, Katie Harron, Lyn Healy, Wishva Herath, Frida Holm, Outi Hovatta, Johan Hyllner, Maneesha S Inamdar, Astrid Kresentia Irwanto, Tetsuya Ishii, Marisa Jaconi, Ying Jin, Susan Kimber, Sergey Kiselev, Barbara B Knowles, Oded Kopper, Valeri Kukharenko, Anver Kuliev, Maria A Lagarkova, Peter W Laird, Majlinda Lako, Andrew L Laslett, Neta Lavon, Dong Ryul Lee, Jeoung Eun Lee, Chunliang Li, Linda S Lim, Tenneille E Ludwig, Yu Ma, Edna Maltby, Ileana Mateizel, Yoav Mayshar, Maria Mileikovsky, Stephen L Minger, Takamichi Miyazaki, Shin Yong Moon, Harry Moore, Christine Mummery, Andras Nagy, Norio Nakatsuji, Kavita Narwani, Steve K W Oh, Sun Kyung Oh, Cia Olson, Timo Otonkoski, Fei Pan, In-Hyun Park, Steve Pells, Martin F Pera, Lygia V Pereira, Ouyang Qi, Grace Selva Raj, Benjamin Reubinoff, Alan Robins, Paul Robson, Janet Rossant, Ghasem H Salekdeh, Thomas C Schulz, Karen Sermon, Jameelah Sheik Mohamed, Hui Shen, Eric Sherrer, Kuldip Sidhu, Shirani Sivarajah, Heli Skottman, Claudia Spits, Glyn N Stacey, Raimund Strehl, Nick Strelchenko, Hirofumi Suemori, Bowen Sun, Riitta Suuronen, Kazutoshi Takahashi, Timo Tuuri, Parvathy Venu, Yuri Verlinsky, Dorien Ward-van Oostwaard, Daniel J Weisenberger, Yue Wu, Shinya Yamanaka, Lorraine Young, Qi Zhou & The International Stem Cell Initiative


The International Stem Cell Initiative compares 125 ethnically diverse human embryonic stem cell lines at early and late passage. Data on karotype, single-nucleotide polymorphisms and methylation shed light on how the cells adapt to long-term culture.


Careers and Recruitment

The challenges of modern interdisciplinary medical research pp1145 - 1148

Philipp von Roth, Benedict J Canny, Hans-Dieter Volk, J Alison Noble, Charles G Prober, Carsten Perka & Georg N Duda


The increasing complexity of medical science poses significant challenges to medical education, leading to a growing gap between medical researchers and treating practitioners.


People p1150